Contacts of the helix formed by residues 211 - 223 (chain D) in PDB entry 4ILW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D LEU* 4.5 9.9 - - + -
129D VAL* 4.0 34.5 - - + +
132D ALA* 4.0 22.2 - - + -
133D ILE* 4.5 3.8 - - + -
162D PHE* 4.1 13.0 - - + -
196D PHE* 3.8 37.7 - - + -
202D TRP* 3.7 25.8 - - + -
203D THR 3.2 16.4 + - - +
209D THR 3.2 2.8 + - - -
210D ASN* 1.3 71.9 - - - +
212D PHE* 1.3 53.5 + - - +
214D VAL 3.3 0.7 + - - -
215D ALA* 2.7 41.6 + - + +
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Residues in contact with PHE 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA* 3.8 23.3 - - + +
135D LYS* 3.7 28.9 - - + -
136D ALA* 3.6 33.6 - - - +
139D VAL* 3.8 17.3 - - + -
203D THR 5.0 0.2 + - - -
210D ASN* 3.4 8.6 - - - +
211D LEU* 1.3 77.9 - - - +
213D LEU* 1.3 84.3 + - + +
215D ALA* 3.8 1.6 - - - +
216D ALA* 2.8 33.4 + - + +
245D LEU* 3.8 24.7 - - + -
248D PHE* 3.9 23.6 - + + -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ASN* 3.1 22.3 - - + +
212D PHE* 1.3 84.6 - - + +
214D VAL* 1.3 63.7 + - + +
216D ALA* 3.7 4.6 - - - +
217D HIS* 3.2 18.4 + - - +
234D LEU* 3.7 10.4 - - + +
239D TYR* 4.8 6.5 - - + +
240D ASN* 3.3 35.6 - - - +
241D SER 4.3 7.6 - - - +
242D PHE 4.0 21.1 - - - +
243D THR 5.4 1.8 - - - +
244D GLU 5.8 0.2 - - - +
245D LEU* 3.7 28.7 - - + -
248D PHE* 3.9 29.2 - - + -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.7 18.4 - - - +
180D LEU* 4.3 12.3 - - + -
181D ALA* 3.6 29.8 - - + -
196D PHE* 3.7 10.8 - - + -
202D TRP* 3.8 21.5 - - + -
209D THR* 4.0 11.9 - - + -
210D ASN 3.3 17.4 + - - +
211D LEU 3.9 0.7 - - - +
213D LEU* 1.3 77.5 - - + +
215D ALA* 1.3 57.6 + - - +
217D HIS* 3.2 4.8 + - - +
218D GLU* 2.9 28.1 + - + +
240D ASN* 5.6 3.6 - - - +
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.4 15.5 - - + -
136D ALA* 3.8 15.7 - - + -
194D ILE* 4.5 1.9 - - + +
196D PHE* 3.7 25.8 - - + -
211D LEU* 2.7 24.1 + - + +
212D PHE* 3.8 4.3 - - - +
214D VAL* 1.3 73.1 - - - +
216D ALA* 1.3 56.9 + - - +
218D GLU* 3.3 3.0 + - - +
219D LEU* 2.8 37.3 + - + +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ALA* 3.5 22.1 - - + +
139D VAL* 4.8 4.5 - - + -
140D TRP* 2.8 31.0 + - - +
212D PHE* 2.8 30.2 + - + +
213D LEU* 3.7 6.1 - - - +
215D ALA* 1.3 74.1 - - - +
217D HIS* 1.3 61.0 + - - +
219D LEU* 4.6 0.4 - - - -
220D GLY 3.3 5.0 + - - -
234D LEU* 3.6 21.3 - - + -
248D PHE* 5.2 1.3 - - + -
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Residues in contact with HIS 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CYS 2.8 6.0 + - - -
2A SER* 3.5 19.3 - - - +
213D LEU 3.2 10.3 + - - +
214D VAL* 3.2 9.3 + - - +
216D ALA* 1.3 75.1 - - - +
218D GLU* 1.3 74.5 + - - +
220D GLY* 3.1 10.2 + - - -
221D HIS* 3.1 3.0 + - - -
227D HIS* 3.4 5.4 - + - -
234D LEU* 2.8 35.6 + - + +
235D MET* 3.4 47.4 - - + +
236D TYR 3.8 9.4 + - - -
237D PRO* 3.8 1.8 - - + -
240D ASN* 4.9 4.6 - - - +
301D ZN 2.0 37.0 - - - -
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Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CYS* 2.9 22.1 + - - -
2A SER* 2.5 39.4 + - - +
181D ALA* 3.5 19.5 - - + +
182D HIS* 3.9 9.4 - - - +
183D ALA* 3.4 18.6 + - + +
194D ILE* 3.8 27.6 - - + -
196D PHE* 4.8 0.2 - - + -
214D VAL* 2.9 22.7 + - + +
215D ALA 3.9 2.5 - - - +
217D HIS* 1.3 79.5 - - - +
219D LEU* 1.3 62.8 + - - +
221D HIS* 3.0 20.8 + - - +
222D SER* 3.1 10.2 + - - -
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 4.5 5.2 - - + +
136D ALA* 3.8 25.4 - - + +
137D LEU* 3.6 41.5 - - + +
140D TRP* 3.7 17.9 - - + +
148D PHE* 5.4 3.1 - - + -
158D ILE* 4.2 25.1 - - + -
160D ILE* 5.2 3.1 - - + -
194D ILE* 3.6 21.3 - - + -
215D ALA* 2.8 23.8 + - + +
217D HIS 3.2 0.2 - - - -
218D GLU* 1.3 73.7 - - - +
220D GLY* 1.3 58.3 + - - +
222D SER* 3.1 3.6 + - - -
223D LEU* 2.9 34.3 + - + +
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Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TRP* 3.6 23.0 - - - +
216D ALA 3.3 5.1 + - - -
217D HIS 3.1 10.9 + - - -
219D LEU* 1.3 77.2 - - - +
221D HIS* 1.3 54.3 + - - +
223D LEU* 3.3 6.0 + - - +
224D GLY 3.2 5.7 + - - -
225D LEU* 2.8 40.6 + - - +
235D MET* 4.0 5.4 - - - -
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Residues in contact with HIS 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A CYS 3.0 12.0 + - - -
69A SER* 4.6 0.4 - - - -
70A ALA* 3.6 32.8 - - + +
183D ALA* 4.0 9.0 - - + +
184D TYR 4.1 1.8 - - - +
185D PRO* 3.5 15.1 - - - +
217D HIS* 3.1 13.3 + + - -
218D GLU* 3.0 17.9 + - - +
220D GLY* 1.3 72.1 - - - +
222D SER* 1.3 61.7 + - - +
224D GLY* 2.9 19.9 + - - -
225D LEU 3.0 26.2 + - - +
226D PHE* 4.0 7.6 - + - -
227D HIS* 3.5 19.5 - + - -
235D MET* 3.6 8.7 - - + +
301D ZN 2.2 36.5 - - - -
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Residues in contact with SER 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D TRP* 2.8 24.4 + - - -
158D ILE* 4.2 16.2 - - - -
183D ALA* 4.4 0.7 - - - +
184D TYR 3.5 11.1 + - - -
186D PRO* 3.3 12.2 - - - +
192D GLY* 2.6 28.8 + - - -
193D ASP 4.1 1.2 + - - -
194D ILE* 3.4 21.5 - - - +
218D GLU 3.1 7.8 + - - -
219D LEU* 3.1 13.9 + - - -
221D HIS* 1.3 76.4 - - - +
223D LEU* 1.3 58.0 + - - +
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D PRO 4.0 0.5 - - - +
108D TRP* 4.0 9.4 - - + +
113D LEU* 3.9 20.6 - - + -
140D TRP* 3.8 37.7 - - + -
146D LEU* 4.1 13.7 - - + -
148D PHE* 3.9 27.6 - - + -
158D ILE* 4.7 4.7 - - + -
186D PRO* 3.6 5.1 - - - +
219D LEU* 2.9 19.4 + - + +
220D GLY 3.7 5.2 - - - +
221D HIS 3.1 0.4 - - - -
222D SER* 1.3 79.2 - - - +
224D GLY* 1.3 54.6 + - - +
258D ILE* 4.0 21.3 - - + -
261D LEU* 3.7 4.0 - - - +
262D TYR* 2.5 32.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il